Replace examples with those from the second edition of the AMUSE book by rieder · Pull Request #1227 · amusecode/amuse

rieder · 2026-03-10T10:50:34Z

Existing examples are outdated, in some cases not working and often duplicated by others.
This replaces all examples from the "textbook", "syllabus" and "simple" directories with the complete set from the textbook (second edition).

rieder · 2026-03-10T10:54:21Z

To be done:

Some tests may use some of the old examples, so these need to be updated
Add installable package for the examples (they should be installable as "amuse-examples" via pip, at the least - living in the amuse.examples namespace, as this is how they are used in the book).
a file "AMUSE_updates.pdf" needs to be added, as a file containing any errata for the book.
missing / later conceived examples may be added later

rieder · 2026-03-10T10:57:48Z

If we do want to keep (some of) the old examples around, they should be in some directory that makes it clear that these are archived, and not updated. If they are still useful, they should be moved to the new structure.

LourensVeen · 2026-03-10T15:31:10Z

I don't see how the tests would depend on the examples, but I'll go and do a local build and run them all to check.

I think pip packages, the PDF, and more examples should be separate Issues, so if it doesn't break the tests then I'll merge this, even if it isn't perfect I doubt it'll make things worse.

LourensVeen

I've pushed a commit to move the examples to src/amuse_examples and add a forward in src/amuse/examples, and make the whole thing an installable package like the others.

Looking at it again, I think it's probably better to put the actual examples into a subdirectory src/amuse_examples/amuse_examples, so that there's nothing else in the directory. Then we can symlink that to /examples, and if anyone plays with it on the command line then they're less likely to mess up the package definitions.

I've run the tests and this didn't break anything, but then I ran the examples themselves and found many problems, which I've added comments for.

LourensVeen · 2026-03-12T13:24:23Z

src/amuse/examples/2017arXiv170307029H_Fig3.py

Crashes with

File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/2017arXiv170307029H_Fig3.py", line 48, in <module> from distinct_colours import get_distinct ModuleNotFoundError: No module named 'distinct_colours'

that is a remnant, should have been removed from the example.

Ah, I actually found the file and put it in as part of my quick fixes. So that should come back out then.

src/amuse/examples/anim_gravity.py

src/amuse/examples/cooling_class.py

src/amuse/examples/gravity_hydro.py

src/amuse/examples/gravity_stellar_minimal.py

src/amuse/examples/star_to_sph.py

LourensVeen · 2026-03-12T14:19:02Z

src/amuse/examples/supernova_grid.py

Won't run using amuse.examples.run:

Traceback (most recent call last): File "<string>", line 1, in <module> from amuse.examples import run ; run('supernova_grid') ~~~^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ~~~~~~~~~~~~^^ TypeError: main() missing 7 required positional arguments: 'stellar_mass', 'stellar_radius', 'core_mass', 'core_radius', 't_end', 'dt', and 'resolution'

If I fix that, it crashes because we're trying to index grid.rho with something that isn't an int:

File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/examples/supernova_grid.py", line 17, in plot_grid rho = grid.rho[:,:,halfway].value_in(units.g/units.cm**3) ~~~~~~~~^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/units/quantities.py", line 666, in __getitem__ return new_quantity(self._number[index], self.unit) ~~~~~~~~~~~~^^^^^^^ IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Lines 16 and 17 look suspicious to me, because there's an ellipsis in the first place on line 16, then halfway is used in the last place on line 17. But I don't know what this does.

LourensVeen · 2026-03-12T14:19:30Z

src/amuse/examples/supernova_sph.py

Fails because prepare_figure is missing.

src/amuse/examples/three_body_bridge_order4m4.py

LourensVeen · 2026-03-12T14:22:19Z

src/amuse/examples/tres_minimal.py

@@ -0,0 +1,55 @@
+from amuse.units import units
+from amuse.community.seba import Seba
+from seculartriple_tps import Seculartriple


seculartriple_tps is missing.

that is part of the TRES package (https://github.com/silviatoonen/tres), maybe fail with an error message if this is not installed

From a quick look, TRES needs to be updated anyway to work with the new AMUSE build system. Won't work as-is. One for my to-do list I guess, if I have the resources.

This seems to be the least ugly way to make python -m amuse.examples.x work

LourensVeen · 2026-03-13T21:00:26Z

Moved the examples to src/amuse/examples because that's the only way to make python -m amuse.examples.<name> work. (Well, I can think of something else, but that's so ugly it's borderline evil.)

Here's a list of example names that occur in the book, but seem to be missing from this PR:

plot_nbody_performance
brutus
run_nbody_precision
plot_stellar_structure
stellar.merger_stellar_density_profile
stellar_isochrone
stellar.massloss_response
plot_stellar_massloss_response
plot_M67withBSS_tracks
plot_solar_comparison
plot_hydro_disk_with_bump
hydro_give_or_take
plot_accretion_from_windy_star
data.fig_star_in_sph_N10000.M1.0MSun.npy
supernova_irradiation
evolve_triple_with_wind
plot_triple_with_wind
gravity_collision
supernova_IIp_Lightcurve
plot_supernova_IIp_and_disk_temperature
gravity_kepler_disks
compare_disk_size_Trapezium
basic_multiples
imbhs_with_friction
gravity_potential
gravity_gravity
plot_sun_and_earth_and_moon
no_bridge_ph4_integrator
three_body_bridge
three_body_bridge_hierachical
three_body_bridge_n_order
solar_cluster_in_galaxy_potential
integrate_sun_in_galaxy_potential
solar_cluster_in_semilive_galaxy
plot_solar_cluster_in_live_galaxy
Sun_and_m67_in_the_galaxy
plot_rlof_triples
xi_tau_rlof
plot_xi_tau_orbital_evolution
make_planets_oligarch
planetary_system
plot_planetary_system
venice_minimal
plot_projected_disk_density_from_top
plot_projected_disk_temp_from_top
plot_sstar_orbits
initialize_sstars
plot_plummer_stars_and_planets
christmas_card_2010
stellar.multiple_stellar_threaded
test_jeans_instability
particles_and_gas_in_cluster
hr_diagram_cluster
gas_in_cluster
pythagorean
kepler_orbiters_planets_around_sun
evolve_orbit_in_potential
evolve_binary
particles_and_multiples
basic_multiples_si
molecular_cloud_chemistry
plot_nbody_performance
mercury_example
h2region
linear_wave
linear_wave_boundaries
solar_cluster_in_live_galaxy
clump_finding
ppd_minimal

This file was deleted from the examples on purpose, the correct fix would be to remove the references to this. The replacement is using the matplotlib style for the book.

rieder · 2026-03-16T12:45:36Z

src/amuse/examples/gravity_to_virial.py

need to remove these references instead.

The use of this is replaced with a dedicated matplotlib stylesheet, need to update examples to use this instead.

LourensVeen · 2026-03-16T14:55:39Z

src/amuse/examples/calculate_core_temperature_density.py

+
+
+def main(**kwargs):
+    calculate_core_temperature_density(**kwargs)


I'm getting

Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/examples/calculate_core_temperature_density.py", line 137, in <module> main(**arguments.__dict__) ~~~~^^^^^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/examples/calculate_core_temperature_density.py", line 132, in main calculate_core_temperature_density(**kwargs) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^ TypeError: calculate_core_temperature_density() got an unexpected keyword argument 'metalicity'

This reverts commit 8148495.

LourensVeen · 2026-03-17T10:10:55Z

I've added back some more missing examples from main. Remaining missing ones that are mentioned in the book but that I can't find:

hr_diagram_cluster   (8.5.3 on page 8-28)
initialize_sstars    (10.4.1 on page 10-25)
integrate_sun_in_galaxy_potential    (9.4.1.2 on page 9-32)
plot_plummer_stars_and_planets    (fig. A.1 on page A-10)
plot_rlof_triples    (fig. 9.13 on 9-38)
plot_solar_cluster_in_live_galaxy    (fig. 9.11 on page 9-35)
plot_sun_and_earth_and_moon    (fig. 9.7 on page 9-23)
plot_xi_tau_orbital_evolution    (fig. 9.14 on page 9-39)
ppd_minimal    (fig. B.3 on page B-15)
run_nbody_precision    (fig. 4.13 on page 4-46)
three_body_bridge_n_order    (table 9.1 on page 9-21)
venice_minimal    (fig. 10.2 on page 10-11)
xi_tau_rlof    (fig. 9.14 on page 9-39)

and then there's data.fig_star_in_sph_N10000.M1.0MSun.npy which is also missing, which is used by plot_single_star_to_sph.py. That single_star_to_sph.py script currently has its write command commented out, so it doesn't produce output, and anyway it uses a different file name.

rieder · 2026-03-17T13:57:52Z

Last missing files (and if found, where they are found):
stellar.merger_stellar_density_profile --> merger_stellar_density_profile.py (wrong name)
data.fig_star_in_sph_N10000.M1.0MSun.npy --> data/fig_star_in_sph_N10000M1.0MSun.npy (missing dot)
compare_disk_size_Trapezium --> compare_disk_size_trapezium.py (capitalization is off)
plot_sun_and_earth_and_moon --> ?
three_body_bridge_hierachical --> three_body_bridge_hierarchical.py (spelling error)
three_body_bridge_n_order --> ?
integrate_sun_in_galaxy_potential --> ?
plot_solar_cluster_in_live_galaxy --> ?
Sun_and_m67_in_the_galaxy --> ?
xi_tau_rlof --> ?
plot_xi_tau_orbital_evolution --> ?
venice_minimal --> ?
initialize_sstars --> ?
stellar.multiple_stellar_threaded --> multiple_stellar_threaded (wrong name)
ppd_minimal --> ?

rieder added 5 commits March 10, 2026 11:41

Remove old examples

012cc51

Remove old examples

b8f821b

remove data from old example

810d6a6

Remove old examples

ff0216e

Add new examples

9d930ad

rieder requested a review from a team as a code owner March 10, 2026 10:50

github-project-automation bot added this to Development Board Mar 10, 2026

github-project-automation bot moved this to Backlog in Development Board Mar 10, 2026

rieder added 2 commits March 10, 2026 12:02

remove more old examples

546e2a7

Further simplify and remove old examples

89f45c2

Create amuse_examples package and forwards from amuse.examples

28b8cda

LourensVeen force-pushed the examples_book_v2 branch from 5d45632 to 28b8cda Compare March 12, 2026 13:22

LourensVeen requested changes Mar 12, 2026

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github-project-automation bot moved this from Backlog to Open PRs in Development Board Mar 12, 2026

LourensVeen mentioned this pull request Mar 12, 2026

Update Galaxia names and fix examples #1223

Merged

LourensVeen self-assigned this Mar 13, 2026

LourensVeen added this to the Release 2026.3.0 milestone Mar 13, 2026

LourensVeen added 3 commits March 13, 2026 11:15

Make subdir for examples to contain the mess when running in-place

af14811

Actually, move examples into the framework

8c0002f

This seems to be the least ugly way to make python -m amuse.examples.x work

Apply various easy fixes

de86dc4

rieder and others added 2 commits March 16, 2026 13:41

add missing examples (incomplete)

12f6927

Delete src/amuse/examples/distinct_colours.py

c387b63

This file was deleted from the examples on purpose, the correct fix would be to remove the references to this. The replacement is using the matplotlib style for the book.

rieder commented Mar 16, 2026

View reviewed changes

src/amuse/examples/gravity_to_virial.py

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need to remove these references instead.

rieder added 3 commits March 16, 2026 13:48

remove internal file

8148495

Remove obsolete prepare_figure.py

b143588

The use of this is replaced with a dedicated matplotlib stylesheet, need to update examples to use this instead.

fixes for gravity_to_virial (incomplete)

006f69a

Merge branch 'main' into examples_book_v2

25cf8ea

LourensVeen reviewed Mar 16, 2026

View reviewed changes

rieder and others added 5 commits March 16, 2026 17:17

fix for example

acfb670

small change

7928883

Revert "remove internal file"

bf6b50e

This reverts commit 8148495.

additional fixes

6f8104e

Add back more missing examples

42dc6d3

rieder added 6 commits March 17, 2026 13:38

update lagrange_points example

85af1a9

additional updates

34ad169

update gravity_potential

dbb6d71

update make_oort_cloud.py

9c3ca0e

add missing example

2fe4b36

add more missing examples

ff7a667



		def main(**kwargs):
		calculate_core_temperature_density(**kwargs)

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rieder commented Mar 17, 2026 •

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